MTA2

metastasis associated 1 family member 2, the group of GATA zinc finger domain containing|NuRD complex subunits|Myb/SANT domain containing

Basic information

Region (hg38): 11:62593214-62601865

Previous symbols: [ "MTA1L1" ]

Links

ENSG00000149480

∙ NCBI:9219 ∙ OMIM:603947 ∙ HGNC:7411 ∙ Uniprot:O94776 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the MTA2 gene.

not_specified (45 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the MTA2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004739.4. Only rare variants are included in the table.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			45 clinvar			45
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	45	0	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
MTA2	protein_coding	protein_coding	ENST00000278823	18	8627

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.745	0.255	125586	0	162	125748	0.000644

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.13	224	400	0.560	0.0000235	4309
Missense in Polyphen		53	144	0.36806		1683
Synonymous	-0.852	157	144	1.09	0.00000753	1358
Loss of Function	4.66	8	39.7	0.202	0.00000209	444

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00163	0.00152
Ashkenazi Jewish	0.000312	0.000298
East Asian	0.00147	0.00141
Finnish	0.000613	0.000601
European (Non-Finnish)	0.000768	0.000730
Middle Eastern	0.00147	0.00141
South Asian	0.0000996	0.0000980
Other	0.000344	0.000326

dbNSFP

Source: dbNSFP

Function: FUNCTION: May be involved in the regulation of gene expression as repressor and activator. The repression might be related to covalent modification of histone proteins.;
Pathway: ERCC6 (CSB) and EHMT2 (G9a) positively regulate rRNA expression;Positive epigenetic regulation of rRNA expression;Signal Transduction;Epigenetic regulation of gene expression;Gene expression (Transcription);Generic Transcription Pathway;HDACs deacetylate histones;RNA Polymerase I Promoter Clearance;RNA Polymerase II Transcription;Chromatin modifying enzymes;RNA Polymerase I Transcription;RNA Polymerase I Transcription Initiation;EGFR1;Regulation of PTEN gene transcription;PTEN Regulation;PIP3 activates AKT signaling;Chromatin organization;Regulation of TP53 Activity through Acetylation;Regulation of TP53 Activity;Transcriptional Regulation by TP53;Intracellular signaling by second messengers;Signaling events mediated by HDAC Class I (Consensus)

Recessive Scores

pRec: 0.278

Intolerance Scores

loftool: 0.204
rvis_EVS: -1.02
rvis_percentile_EVS: 7.94

Haploinsufficiency Scores

pHI: 0.896
hipred: Y
hipred_score: 0.809
ghis: 0.627

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: S
essential_gene_gene_trap: K
gene_indispensability_pred: E
gene_indispensability_score: 0.768

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Mta2
Phenotype: immune system phenotype; renal/urinary system phenotype; skeleton phenotype; liver/biliary system phenotype; hematopoietic system phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); craniofacial phenotype; homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype;

Gene ontology

Biological process: negative regulation of transcription by RNA polymerase II;DNA methylation;chromatin assembly or disassembly;regulation of fibroblast migration;histone deacetylation;ATP-dependent chromatin remodeling;positive regulation of transcription by RNA polymerase II
Cellular component: histone deacetylase complex;nuclear chromatin;nucleus;nucleoplasm;transcription factor complex;membrane;NuRD complex;protein-containing complex
Molecular function: transcription regulatory region sequence-specific DNA binding;DNA-binding transcription factor activity, RNA polymerase II-specific;RNA polymerase II transcription factor binding;RNA polymerase II repressing transcription factor binding;transcription coactivator activity;transcription corepressor activity;histone deacetylase activity;protein binding;zinc ion binding;nucleosomal DNA binding;histone deacetylase binding